Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

Basic information

species Zea mays
transcript GRMZM2G086015_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatag--cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
|| |||||||| || || | ||| | |||    |  | |    |||| | ||||   ||||||| ||    |||| | ||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||||
gtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagca--tctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
      | |  || |      |  | |      |||   ||| || |    ||   | || ||||  || ||| |   ||  | |||||| || || |||||| | ||| | || ||||||||||||||||| |||||||||||||| ||||||||    || ||  ||||| || |||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgtttatcaattttttttct-cagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatct------gttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
        |      | ||||| ||    |  ||   |  ||||        ||||     | | |    ||  | ||    |||||| || || |||||  ||||| | ||||||||||| |||||||| ||||| |||||||| ||||||||    || ||  ||||| || |||| || || 
-------gtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagca--tctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
      | |  || |      |  | |      |||   ||| |  |    ||   |||| ||||  || ||| | | ||    |||||| || || |||||| | ||| | || ||||||||||||||||| |||||||||||||| ||||||||    || ||  | ||| |  |||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctgtttatcaa-ttgtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
--------------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
               |||||||  | || |    || ||  | |    |  |  || || |||  | | |  ||      | |     | ||||||||| || || ||  | || || ||  ||||||| |||||||| ||||||||||| || |||||||||   || ||  |||||||| |  | || || 
gtacgttcctttatatatgtttatttgaga---ctgttttatcttgcatacataatttgctaacatatttccctttttcttgg--gaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagctt----ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
||| ||  | | ||      || ||   |   |  |     |||   | |||||    ||        | ||    | | |||||| || |||||||| ||  | || ||  |||||||||||||||| ||||||||||| || ||||| ||  | || |   |||| ||| |  | || || 
gtaagtgct-tagatttgtgtgtttatataattgagattgttctagaagtttctgatgctgttcccctgttttgtggatgcagTGTTATAGGGTACACCTTGTTGCTAAGCCTGATTGAGTACAAGACTCTTGTGATGCGGGGTGATTTAGACAAAGCCAGTGAAATCTTACCTACAATTCCT

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
        |||||||   |  |  | ||||  |  |  ||||||  |  |  | | |||| || | |    ||   |    ||||||| ||||| ||||| |||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || ||  || | ||| | || || || 
gtaagcagatgttttactgttatgattgctaacaatgttttgta--acttactgacttctgtgtccactttatgatt----acagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagctt----------ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
      | |  |||    ||||       |         |||| | || || |||  ||| | | ||  || | | ||            | ||||||||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || 
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtat-tgctaacatcttt-attattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC

upper sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctga-ctaa-------caaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
||  |    || |  | |    ||||       |    || | ||||  | |   ||| ||||        |  |    |  | |||||| || || || || |||||||| | |||||||||||||||||| ||||| |||||||| || ||  | | |||||   |||||||| | |  || || 
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|9952611|gb|BE639299.1|BE639299
EST:     CGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
genomic: CGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
EST: gi|67024352|gb|CO453101.1|CO453101
EST:     GGATATATTGCGCACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 180

ACTTACAGGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 60

ACTTACAGGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 64

ACTTACAGGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 107

ACTTACAGGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA
                                gactaac  putative branch site (score: 107)
                   tgttaattt  TA-rich tract